Contacts of the strand formed by residues 306 - 314 (chain A) in PDB entry 3UAJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A CYS* 3.6 22.7 - - + -
304A GLY 3.9 10.1 + - - -
305A LYS* 1.3 83.1 + - - +
307A SER* 1.3 60.6 + - - +
324A VAL* 4.0 20.0 - - + -
325A LYS 3.4 15.9 - - - -
326A TYR* 3.4 41.3 - + + -
327A GLU* 5.0 0.9 - - - -
335A VAL* 3.6 34.1 - - + -
336A PRO* 3.9 10.8 - - + -
358A ALA* 4.6 1.6 - - + -
365A THR* 5.8 0.9 - - - -
380A ILE* 4.0 26.2 + - + +
381A GLY* 4.3 14.8 - - - -
385A SER 5.1 2.2 + - - +
386A ALA* 6.2 0.4 - - - +
387A LEU* 3.5 25.6 + - + +
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LYS* 5.5 3.6 - - - -
306A PHE* 1.3 74.3 - - - +
308A ILE* 1.3 64.2 + - - +
309A ASP 3.3 0.7 + - - -
324A VAL* 3.4 4.3 - - - -
325A LYS* 2.8 50.4 + - - +
327A GLU* 2.8 26.3 + - - -
387A LEU* 4.6 6.3 - - - -
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Residues in contact with ILE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A SER* 1.3 69.6 - - - +
309A ASP* 1.3 64.9 + - - +
310A LYS 4.2 4.7 - - - +
311A GLU* 4.7 22.2 - - + +
312A MET 5.7 0.2 - - - +
322A VAL* 3.9 15.5 - - + -
323A LYS 3.5 4.0 - - - +
324A VAL* 3.8 16.4 - - + -
387A LEU* 3.8 26.9 - - + +
389A LEU* 3.9 28.9 - - + -
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Residues in contact with ASP 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A SER 3.3 3.6 + - - -
308A ILE* 1.3 72.7 - - - +
310A LYS* 1.3 59.4 + - - +
323A LYS* 2.8 22.5 + - + +
324A VAL 4.5 0.7 - - - +
325A LYS* 3.9 22.6 + - + +
364A VAL* 3.5 43.2 - - + +
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Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ILE* 4.2 5.9 - - - +
309A ASP* 1.3 79.7 - - - +
311A GLU* 1.4 68.3 + - - +
322A VAL* 3.7 6.1 - - - +
323A LYS* 3.5 45.1 + - + +
101B TRP* 3.4 71.0 + - + +
104B GLY* 6.1 0.6 - - - -
105B CYS 4.2 6.8 + - - +
106B GLY* 5.0 7.2 - - - -
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ILE* 4.7 18.7 - - + +
310A LYS* 1.4 75.5 - - - +
312A MET* 1.3 76.3 + - - +
313A ALA* 3.4 2.3 + - - +
322A VAL* 5.2 0.2 - - - -
389A LEU* 5.8 5.2 - - + -
391A TRP* 5.2 4.3 - - - -
101B TRP* 3.2 21.9 + - - -
106B GLY 5.2 1.2 - - - +
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Residues in contact with MET 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A ILE* 5.7 0.4 - - - +
310A LYS 3.7 1.6 + - - -
311A GLU* 1.3 85.5 - - + +
313A ALA* 1.3 60.9 + - - +
320A THR* 3.8 27.4 - - + +
321A VAL 3.4 15.3 - - - +
322A VAL* 3.8 20.4 - - + +
369A LEU* 3.9 20.9 - - - -
378A ILE* 3.8 28.9 - - + -
380A ILE* 6.2 0.2 - - - -
389A LEU* 4.9 23.7 - - + +
390A HIS 5.1 0.4 - - - +
391A TRP* 3.5 54.2 - - + -
107B LEU* 5.8 0.5 - - - +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A GLU 3.4 1.9 + - - +
312A MET* 1.3 74.1 - - - +
314A GLU* 1.3 61.6 + - - +
315A THR 3.9 0.5 + - - -
320A THR* 3.4 3.1 - - - -
321A VAL 3.0 29.9 + - - +
391A TRP* 4.4 4.3 - - - -
101B TRP* 3.8 9.4 - - + +
106B GLY 3.6 23.8 - - - +
107B LEU* 4.3 15.3 - - + -
108B PHE* 3.8 22.8 - - + -
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Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ALA* 1.3 72.5 - - - +
315A THR* 1.3 73.0 + - - +
318A GLY* 3.6 26.5 - - - +
319A THR 3.6 3.4 - - - +
320A THR* 4.0 6.3 - - + -
391A TRP* 3.6 28.7 + - + -
392A PHE 4.6 1.0 - - - +
393A ARG* 3.5 30.6 - - - +
394A LYS 4.9 1.4 + - - -
107B LEU* 4.9 7.3 - - + +
108B PHE* 3.3 24.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il